Integrated Analysis of Transcriptome and Metabolome Reveals Molecular Mechanisms of Rice with Different Salinity Tolerances

Rice is a crucial global food crop, but it lacks natural tolerance to high salt levels, resulting in significant yield reductions. To gain comprehensive understanding of the molecular mechanisms underlying rice’s tolerance, further research required. In this study, transcriptomic and metabolomic differences between salt-tolerant rice variety Lianjian5 (TLJIAN) salt-sensitive Huajing5 (HJING) were examined. Transcriptome analysis revealed 1518 differentially expressed genes (DEGs), including 46 previously reported salt-tolerance-related genes. Notably, most transcription factors, such as NAC, WRKY, MYB, EREBP, upregulated rice. Metabolome identified 42 accumulated metabolites (DAMs) that TLJIAN, flavonoids, pyrocatechol, lignans, lipids, trehalose-6-phosphate, whereas majority organic acids downregulated TLJIAN. The interaction network 29 transporter 19 showed positive correlation calcium/cation exchange protein (OsCCX2 CCX5_Ath) ABC gene AB2E_Ath with multiple DAMs variety. Similarly, factors 6 NACs, 13 AP2/ERFs, WRKY positively correlated 3 lipid oleamide. These results suggested combined effects genes, contribute enhancement Moreover, study provides valuable gene–metabolite reference for mechanism